source: branches/lib/GDE/MUSCLE/src/distpwkimura.cpp

#include "muscle.h"
#include "distfunc.h"
#include "msa.h"
#include "seqvect.h"
#include "pwpath.h"

void DistPWKimura(const SeqVect &v, DistFunc &DF)
        {
        SEQWEIGHT SeqWeightSave = GetSeqWeightMethod();
        SetSeqWeightMethod(SEQWEIGHT_Henikoff);

        const unsigned uSeqCount = v.Length();
        DF.SetCount(uSeqCount);

        const unsigned uPairCount = (uSeqCount*(uSeqCount + 1))/2;
        unsigned uCount = 0;
        SetProgressDesc("PWKimura distance");
        for (unsigned uSeqIndex1 = 0; uSeqIndex1 < uSeqCount; ++uSeqIndex1)
                {
                const Seq &s1 = v.GetSeq(uSeqIndex1);
                MSA msa1;
                msa1.FromSeq(s1);
                for (unsigned uSeqIndex2 = 0; uSeqIndex2 < uSeqIndex1; ++uSeqIndex2)
                        {
                        if (0 == uCount%20)
                                Progress(uCount, uPairCount);
                        ++uCount;
                        const Seq &s2 = v.GetSeq(uSeqIndex2);
                        MSA msa2;
                        msa2.FromSeq(s2);
                
                        PWPath Path;
                        MSA msaOut;
                        AlignTwoMSAs(msa1, msa2, msaOut, Path, false, false);

                        double dPctId = msaOut.GetPctIdentityPair(0, 1);
                        float f = (float) KimuraDist(dPctId);

                        DF.SetDist(uSeqIndex1, uSeqIndex2, f);
                        }
                }
        ProgressStepsDone();

        SetSeqWeightMethod(SeqWeightSave);
        }